Zinc in PDB 6aek: Crystal Structure of ENPP1 in Complex with Papg

The structure of Crystal Structure of ENPP1 in Complex with Papg, PDB code: 6aek was solved by K.Kato, H.Nishimasu, S.Hirano, H.Hirano, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.00 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.486, 94.071, 74.680, 90.00, 96.86, 90.00
R / Rfree (%)	18.3 / 20.8

The structure of Crystal Structure of ENPP1 in Complex with Papg also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Chlorine	(Cl)	6 atoms

The binding sites of Zinc atom in the Crystal Structure of ENPP1 in Complex with Papg (pdb code 6aek). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of ENPP1 in Complex with Papg, PDB code: 6aek:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of ENPP1 in Complex with Papg


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of ENPP1 in Complex with Papg within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1009 b:32.6 occ:1.00 OP3 A:A1007 2.0 32.4 1.0 NE2 A:HIS517 2.1 31.2 1.0 NE2 A:HIS362 2.1 37.9 1.0 OD1 A:ASP358 2.2 30.4 1.0 OD2 A:ASP358 2.3 28.8 1.0 CG A:ASP358 2.6 30.3 1.0 OP2 A:A1007 2.8 35.6 1.0 P A:A1007 3.0 40.6 1.0 CE1 A:HIS517 3.0 30.6 1.0 CD2 A:HIS362 3.0 37.4 1.0 CD2 A:HIS517 3.2 29.1 1.0 CE1 A:HIS362 3.2 36.1 1.0 OP1 A:A1007 3.9 32.9 1.0 CE1 A:HIS406 4.0 32.2 1.0 CB A:ASP358 4.1 31.0 1.0 O2' A:G1008 4.1 76.4 1.0 O5' A:A1007 4.1 36.1 1.0 ZN A:ZN1010 4.1 38.6 1.0 ND1 A:HIS517 4.2 27.3 1.0 CG A:HIS362 4.2 36.5 1.0 NE2 A:HIS406 4.2 34.5 1.0 ND1 A:HIS362 4.3 35.8 1.0 CG A:HIS517 4.3 27.4 1.0 C5' A:A1007 4.3 36.0 1.0 OD1 A:ASP200 4.5 40.1 1.0 CE A:MET408 4.6 27.1 1.0 C2' A:G1008 4.7 75.8 1.0 O A:ASP358 4.8 28.8 1.0 CA A:ASP358 4.9 32.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of ENPP1 in Complex with Papg


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of ENPP1 in Complex with Papg within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1010 b:38.6 occ:1.00 OD1 A:ASP200 1.9 40.1 1.0 OP2 A:A1007 2.0 35.6 1.0 OD2 A:ASP405 2.0 31.6 1.0 NE2 A:HIS406 2.1 34.5 1.0 CG A:ASP200 2.6 37.7 1.0 OD2 A:ASP200 2.7 37.8 1.0 CG A:ASP405 2.9 30.9 1.0 CE1 A:HIS406 2.9 32.2 1.0 CD2 A:HIS406 3.1 30.1 1.0 OD1 A:ASP405 3.2 30.2 1.0 CB A:ALA238 3.4 25.8 1.0 P A:A1007 3.4 40.6 1.0 CA A:ALA238 3.7 26.1 1.0 OD1 A:ASP358 3.8 30.4 1.0 N A:GLY201 4.0 28.5 1.0 CB A:ASP200 4.0 34.5 1.0 ND1 A:HIS406 4.0 28.7 1.0 CG A:ASP358 4.0 30.3 1.0 N A:ALA238 4.1 26.9 1.0 OP1 A:A1007 4.1 32.9 1.0 ZN A:ZN1009 4.1 32.6 1.0 CG A:HIS406 4.1 30.1 1.0 O5' A:A1007 4.3 36.1 1.0 CB A:ASP405 4.3 29.1 1.0 CE1 A:HIS517 4.3 30.6 1.0 OP3 A:A1007 4.3 32.4 1.0 OD2 A:ASP358 4.4 28.8 1.0 CA A:ASP200 4.4 33.3 1.0 NE2 A:HIS517 4.5 31.2 1.0 C A:ASP200 4.5 30.8 1.0 CA A:GLY201 4.6 27.9 1.0 C5' A:A1007 4.6 36.0 1.0 CB A:ASP358 4.6 31.0 1.0 CE1 A:HIS242 4.6 28.4 1.0 C A:LYS237 4.8 27.4 1.0

K.Kato, H.Nishimasu, D.Oikawa, S.Hirano, H.Hirano, G.Kasuya, R.Ishitani, F.Tokunaga, O.Nureki. Structural Insights Into Cgamp Degradation By Ecto-Nucleotide Pyrophosphatase Phosphodiesterase 1. Nat Commun V. 9 4424 2018.
ISSN: ESSN 2041-1723
PubMed: 30356045
DOI: 10.1038/S41467-018-06922-7